Alignment of HL_67667.2 sequences from 3D to the JAR3D model

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The correspondence between sequences from 3D structures and the motif group is shown in blue and the JAR3D alignment of the sequences to the motif group is shown in black. Occasionally the two disagree, in which case the JAR3D alignment is shown in red.
Column number:
Node in JAR3D model:
Insertion positions indicated by I:
Position in motif group:		1
1
I

2
2

1
3
2
I

4
3

2
5
3
I

6
3

3
7
2
I

8
2

4
9
1
I


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HL_67667.2_Instance_1 HL_67667.2,HL_7PMQ_004,C30_G36CUGUUCG
HL_67667.2_Sequence_1 HL_67667.27PMQ_C30_G36CUGUUCGtrue100000.00
HL_67667.2_Instance_2 HL_67667.2,HL_7PMM_002,C21_G27CUGUUCG
HL_67667.2_Sequence_2 HL_67667.27PMM_C21_G27CUGUUCGtrue100000.00
HL_67667.2_Instance_3 HL_67667.2,HL_3MOJ_002,C2551_G2557CUGUUCG
HL_67667.2_Sequence_3 HL_67667.23MOJ_C_2551_G_2557CUGUUCGtrue100000.00

Conserved interactions between motif group positions in HL_67667.2:
1 4 cWW 
2 3 s35
JAR3D SCFG/MRF model for HL_67667.2:
Character Definition | A,C,G,U,* // Identity and order of characters in matrices
InitialNode  | Left Length Distribution [0.999900000,0.000100000] | Left Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Right Length Distribution [0.999900000,0.000100000] | Right Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Left Index [1] | Right Index [4] // Initial node
BasepairNode | Deletion Probability [0.0000000000030005] | Pair Probability [[0.009443990,0.016935343,0.010857030,0.196859360,0.000000000],[0.020079540,0.009618431,0.236072779,0.013656751,0.000000000],[0.010978957,0.201101150,0.002069466,0.023238378,0.000000000],[0.199411444,0.013158017,0.026511334,0.010008030,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.000000000,0.000000000,0.016116035,0.966962127,0.016116035,0.000805802] | Left Letter Distribution [0.045454545,0.045454545,0.318181818,0.590909091,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [4] // Basepair C30 - G36 cWW 
HairpinNode  | Num Bases [2] | Left Index [2] | Right Index [3] | Norm Constant [1.000000000000000] // Hairpin node U34:C35
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.100000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.100000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.700000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U34
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.100000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.700000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.100000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.100000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C35
Sequences of instances from HL_67667.2:
> HL_67667.2  7PMQ C   30 G   36
CUGUUCG
> HL_67667.2  7PMM C   21 G   27
CUGUUCG
> HL_67667.2  3MOJ C 2551 G 2557
CUGUUCG